Bypass permissions mode still prompts for settings.json edits and other operations

Bug Description

With ALL of the following enabled, Claude Code still prompts for permissions:

• Bypass Permissions mode is ON for the session
• Dangerously Skip Permissions is enabled
• skipDangerousModePermissionPrompt: true in settings.json
• skipAutoPermissionPrompt: true in settings.json
• permissions.defaultMode: "bypassPermissions" in settings.json
• Explicit allow rules for all tool types in settings.json

Claude Code still shows "Do you want to make this edit?" prompts, particularly when editing settings.json but also for other operations intermittently.

Expected Behavior

When bypass permissions mode is active, NO permission prompts should appear for ANY operation. The user has explicitly opted into fully autonomous operation.

Actual Behavior

Permission prompts still appear despite every possible setting being configured to disable them. The settings.json self-edit protection appears to be hardcoded and cannot be bypassed even in bypass permissions mode.

Steps to Reproduce

1. Enable bypass permissions mode
2. Set all permission-related settings to their most permissive values
3. Have Claude edit ~/.claude/settings.json
4. A permission prompt appears despite bypass mode being active

Environment

• Claude Code version: 2.1.89
• OS: macOS Darwin 25.4.0
• Mode: Bypass Permissions (dangerously skip)

Impact

This makes fully autonomous workflows impossible. When using Claude Code for extended autonomous sessions, any unexpected permission prompt blocks progress until a human intervenes.

Screenshot

The prompt shows: "Do you want to make this edit to settings.json?" with options 1. Yes, 2. Yes and allow Claude to edit its own settings for this session, 3. No